Just looking at them casually, they would seem to be the same frame. But there must be some justification to them making the differentiation between the two.

Just looking at them casually, they would seem to be the same frame. But there must be some justification to them making the differentiation between the two.
I thought it was the tubing but I just got back my my LBS and the Allez Pro they have has a sticker that has "E5" on it and I thought that was the difference. I'm am not so sure now.

I have a 2003 S-Works Sapone and a 2002 Alez Pro SLX; both E5 material. The welding is a little different and the tubing shape is different. Top tube and front down tube are not round in diameter on the S-works but more areo, they are round on the Alez Pro. Weight is very similar; my Alez Pro has a normal seatpost binder where the S-works has the wedge shaped compression device. Most importantly, the S-works has a headtube that is 10mm shorter than the Alez at the same 56 size. Hence the geometry is a little different and you lay a little lower in your overall position. It took me a while to figure this out as I was trying to achieve the same seatoing position on both bikes. Also, the Alez Pro comes with a C3 composite fork, the S-works comes with a full carbon C4 fork.
When all was set and done, I have never been able to go as fast on my Alez Pro build out with similar compponents and using the same wheels than on my S-works. No, its not just in my mind! I am actually measuring power output at the chain and with the same power on the chain, I go about 0.5mile/h faster on the S-works bike. Position... I don;t know. Was trying to make them as similar as possible. If you are starting from scratch and are just getting a frame, go on Ebay and get the S-works frame! The better fork is almost worth the exta $200 for the frame. I use the Alex Pro as a backup bike and have it on the trainer all winter. I also take it on trips. Its a bit too good as a beater bike but it clearly does not perform as well as the S-works. On the positive side, the silver/black frame of the Pro looks very nice and very grown up! I actually prefer the looks of the Alez Pro over the S-works. I guess the 2004 S-works comes closer but is still not as sharp as the Alez Pro SLX.

But after reading your post, I actually went to the Specialized web site and compared geometry between the two frames. And there is a difference. As you stated, the headtube is 10mm shorter on the S-works bike. The wheelbase is also 5 mm shorter, and the standover height is actually 4mm less. Minor little changes, but I am sure that they are noticeable while riding. These measurements were taken off of the 52cm frame size. I chose it as that is the size frame that I ride. Seems that the Allez, would be a bit more of a comfortable bike with the taller head tube. I run spacers on mine as it is so the S-works would just make me add 1cm more of spacers and I would recieve no aero benefit from the shorter headtube. The shorter wheelbase would make for a more nimble and quicker handling bike. That is about the only benefit that I could see for a rec rider like myself.